Epoch definition

Epochs were defined to determine which time periods were used to generate weights and which were used to model different periods of vaccination. To generate weights, the MA data from 2000–2001 were defined as pre-vaccine epoch (E1) because PCV7 started rollout for children in 2000, and we considered that this vaccine had not yet perturbed the bacterial population; 2003–2009 as post-PCV7 epoch (E2); and 2010–2014 as post-PCV13 epoch (E3). With the Southwest US data, we defined 1998–2001, 2006–2008, and 2010–2012 as E1, E2, and E3, respectively. With the IPD data, for the weight development, we defined 1998–2000 as E1, 2009 as E2, and 2013–2018 as E3. The pre-vaccine (E1) from the three data sets were used to create weights. Then, E1, E2, and E3 were used to evaluate the impacts of weights on accessory gene frequencies before and after weighting.

To use IPD data to predict post-PCV13 population dynamics, we defined 2009 as the pre-vaccine period for PCV13 (Pre-PCV13 E1), assuming that the population had reached a new equilibrium post-PCV7; 2013–2016 as Post-PCV13 E2, the removal stage of vaccine types in the population; and 2017–2018 as Post-PCV13 E3, assuming that the new equilibrium post-PCV13 had been reached. In this study, the NFDS model attempted to predict the strain proportions in 2017–2018, as this was the longest time period after the introduction of PCV13 for which data were available. Specific data distribution by year, geographic location, and population, as well as detailed data sets used to create weights and conduct the NFDS prediction model, can be found in Supplemental Data 1.